data_4576 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of [d(CGC)r(aaa)d(TTTGCG)]2 Hybrid Junctions Flanked by DNA Duplexes ; _BMRB_accession_number 4576 _BMRB_flat_file_name bmr4576.str _Entry_type original _Submission_date 2000-01-27 _Accession_date 2000-01-27 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hsu Shang-Te . . 2 Chou Mei-Tsen . . 3 Cheng Jya-Wei . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 104 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-19 update BMRB 'update DNA residue label to two-letter code' 2000-05-25 original author 'original release' stop_ _Original_release_date 2015-08-05 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Hydration of [d(CGC)r(aaa)d(TTTGCG)]2 ; _Citation_status 'in press' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hsu Shang-Te . . 2 Chou Mei-Tsen . . 3 Chou Shan-Ho . . 4 Huang Wen-Chang . . 5 Cheng Jya-Wei . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of Molecular Biology' _Journal_volume . _Journal_issue na _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2000 _Details . loop_ _Keyword Hybrid Hydration stop_ save_ ################################## # Molecular system description # ################################## save_chimeric_hybrid_duplex _Saveframe_category molecular_system _Mol_system_name 'a3T3 hybrid' _Abbreviation_common 'chimeric hybrid DNA-RNA duplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'CHDA 1' $CHDA_1 'CHDA 2' $CHDA_1 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state duplex _System_paramagnetic no _System_thiol_state 'not present' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'CHDA 1' 1 'CHDA 2' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_CHDA_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA/RNA chimeric hybrid duplex' _Name_variant 'CH strand A 1-12' _Abbreviation_common 'CHDA 1' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; CGCAAATTTGCG ; loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DC 4 A 5 A 6 A 7 DT 8 DT 9 DT 10 DG 11 DC 12 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_A _Saveframe_category polymer_residue _Mol_type 'RNA linking' _Name_common ADENOSINE-5'-MONOPHOSPHATE _BMRB_code . _PDB_code A _Standard_residue_derivative . _Molecular_mass 347.221 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Jul 18 10:34:56 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons OP3 OP3 O . 0 . ? P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? O2' O2' O . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? N6 N6 N . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? HOP3 HOP3 H . 0 . ? HOP2 HOP2 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2' H2' H . 0 . ? HO2' HO2' H . 0 . ? H1' H1' H . 0 . ? H8 H8 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H2 H2 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING OP3 P ? ? SING OP3 HOP3 ? ? DOUB P OP1 ? ? SING P OP2 ? ? SING P O5' ? ? SING OP2 HOP2 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' O2' ? ? SING C2' C1' ? ? SING C2' H2' ? ? SING O2' HO2' ? ? SING C1' N9 ? ? SING C1' H1' ? ? SING N9 C8 ? ? SING N9 C4 ? ? DOUB C8 N7 ? ? SING C8 H8 ? ? SING N7 C5 ? ? SING C5 C6 ? ? DOUB C5 C4 ? ? SING C6 N6 ? ? DOUB C6 N1 ? ? SING N6 H61 ? ? SING N6 H62 ? ? SING N1 C2 ? ? DOUB C2 N3 ? ? SING C2 H2 ? ? SING N3 C4 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $CHDA_1 . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $CHDA_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $CHDA_1 . mM . stop_ save_ ############################ # Computer software used # ############################ save_Xwinnmr _Saveframe_category software _Name xwinnmr _Version . _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _Sample_label $sample_1 save_ save_1H-1H_ROESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H ROESY' _Sample_label $sample_1 save_ save_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H TOCSY' _Sample_label $sample_1 save_ save_1H-1H_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H DQF-COSY' _Sample_label $sample_1 save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H ROESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H DQF-COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 0.1 n/a temperature 278 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio _Indirect_shift_ratio_citation_label _Correction_value_citation_label DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 $entry_citation $entry_citation stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details ; Three C2'-OH chemical shifts of the RNA adenines were assigned and additional bond orientations were proposed according to their NOEs with neighboring protons. ; loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'CHDA 1' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 DC H41 H 8.09 . 2 2 . 1 DC H42 H 6.99 . 2 3 . 1 DC H5 H 5.74 . 1 4 . 1 DC H6 H 7.52 . 1 5 . 1 DC H1' H 5.61 . 1 6 . 1 DC H2' H 1.87 . 1 7 . 1 DC H2'' H 2.32 . 1 8 . 1 DC H3' H 4.62 . 1 9 . 1 DC H4' H 3.99 . 1 10 . 2 DG H1 H 13.0 . 1 11 . 2 DG H8 H 7.87 . 1 12 . 2 DG H1' H 5.79 . 1 13 . 2 DG H2' H 2.59 . 1 14 . 2 DG H2'' H 2.65 . 1 15 . 2 DG H3' H 4.90 . 1 16 . 2 DG H4' H 4.29 . 1 17 . 3 DC H41 H 8.27 . 2 18 . 3 DC H42 H 6.42 . 2 19 . 3 DC H5 H 5.32 . 1 20 . 3 DC H6 H 7.25 . 1 21 . 3 DC H1' H 5.61 . 1 22 . 3 DC H2' H 2.05 . 1 23 . 3 DC H2'' H 2.29 . 1 24 . 3 DC H3' H 4.78 . 1 25 . 3 DC H4' H 4.55 . 1 26 . 4 A H2 H 6.87 . 1 27 . 4 A H61 H 7.65 . 2 28 . 4 A H62 H 6.31 . 2 29 . 4 A H8 H 8.14 . 1 30 . 4 A H1' H 5.68 . 1 31 . 4 A H2' H 4.82 . 1 32 . 4 A HO2' H 6.51 . 1 33 . 4 A H3' H 4.13 . 1 34 . 4 A H4' H 4.46 . 1 35 . 5 A H2 H 7.20 . 1 36 . 5 A H61 H 7.50 . 2 37 . 5 A H62 H 6.44 . 2 38 . 5 A H8 H 7.99 . 1 39 . 5 A H1' H 5.80 . 1 40 . 5 A H2' H 4.42 . 1 41 . 5 A HO2' H 6.77 . 1 42 . 5 A H3' H 4.51 . 1 43 . 5 A H4' H 4.18 . 1 44 . 6 A H2 H 7.71 . 1 45 . 6 A H61 H 7.47 . 2 46 . 6 A H62 H 6.81 . 2 47 . 6 A H8 H 7.62 . 1 48 . 6 A H1' H 5.64 . 1 49 . 6 A H2' H 4.28 . 1 50 . 6 A HO2' H 6.89 . 1 51 . 6 A H3' H 4.42 . 1 52 . 6 A H4' H 4.19 . 1 53 . 7 DT H3 H 14.1 . 1 54 . 7 DT H6 H 7.31 . 1 55 . 7 DT H71 H 1.43 . 2 56 . 7 DT H72 H 1.43 . 2 57 . 7 DT H73 H 1.43 . 2 58 . 7 DT H1' H 5.68 . 1 59 . 7 DT H2' H 2.11 . 1 60 . 7 DT H2'' H 2.51 . 1 61 . 7 DT H3' H 4.56 . 1 62 . 7 DT H4' H 4.14 . 1 63 . 8 DT H3 H 13.6 . 1 64 . 8 DT H6 H 7.56 . 1 65 . 8 DT H71 H 1.68 . 2 66 . 8 DT H72 H 1.68 . 2 67 . 8 DT H73 H 1.68 . 2 68 . 8 DT H1' H 6.10 . 1 69 . 8 DT H2' H 2.15 . 1 70 . 8 DT H2'' H 2.60 . 1 71 . 8 DT H3' H 4.81 . 1 72 . 8 DT H4' H 4.24 . 1 73 . 9 DT H3 H 13.2 . 1 74 . 9 DT H6 H 7.32 . 1 75 . 9 DT H71 H 1.82 . 2 76 . 9 DT H72 H 1.82 . 2 77 . 9 DT H73 H 1.82 . 2 78 . 9 DT H1' H 5.88 . 1 79 . 9 DT H2' H 2.11 . 1 80 . 9 DT H2'' H 2.43 . 1 81 . 9 DT H3' H 4.87 . 1 82 . 9 DT H4' H 4.13 . 1 83 . 10 DG H1 H 12.4 . 1 84 . 10 DG H8 H 7.80 . 1 85 . 10 DG H1' H 5.77 . 1 86 . 10 DG H2' H 2.55 . 1 87 . 10 DG H2'' H 2.59 . 1 88 . 10 DG H3' H 4.94 . 1 89 . 10 DG H4' H 4.34 . 1 90 . 11 DC H41 H 8.24 . 2 91 . 11 DC H42 H 6.56 . 2 92 . 11 DC H5 H 5.31 . 1 93 . 11 DC H6 H 7.28 . 1 94 . 11 DC H1' H 5.65 . 1 95 . 11 DC H2' H 1.87 . 1 96 . 11 DC H2'' H 2.27 . 1 97 . 11 DC H3' H 4.78 . 1 98 . 11 DC H4' H 4.13 . 1 99 . 12 DG H8 H 7.87 . 1 100 . 12 DG H1' H 6.06 . 1 101 . 12 DG H2' H 2.29 . 1 102 . 12 DG H2'' H 2.54 . 1 103 . 12 DG H3' H 4.61 . 1 104 . 12 DG H4' H 4.12 . 1 stop_ save_